MASON_METHYLATION

NAME

mason_methylation - Methylation Level Simulation

SYNOPSIS

mason_methylation [OPTIONS] -i IN.fa -o OUT.fa

DESCRIPTION

Simulate methylation levels for IN.fa and write them to OUT.fa.

OPTIONS

-h, --help

Display the help message.

--version

Display version information.

-q, --quiet

Low verbosity.

-v, --verbose

Higher verbosity.

-vv, --very-verbose

Highest verbosity.

--seed INTEGER

Seed for RNG. Default: 0.

-i, --in INPUT_FILE

Input FASTA file with genome. Valid filetypes are: .sam[.*], .raw[.*], .gbk[.*], .frn[.*], .fq[.*], .fna[.*], .ffn[.*], .fastq[.*], .fasta[.*], .faa[.*], .fa[.*], .embl[.*], and .bam, where * is any of the following extensions: gz, bz2, and bgzf for transparent (de)compression.

-o, --out INPUT_FILE

Input FASTA file with genome. Valid filetypes are: .sam[.*], .raw[.*], .frn[.*], .fq[.*], .fna[.*], .ffn[.*], .fastq[.*], .fasta[.*], .faa[.*], .fa[.*], and .bam, where * is any of the following extensions: gz, bz2, and bgzf for transparent (de)compression.

Methylation Level Simulation:

--methylation-levels

Enable methylation level simulation.

--meth-cg-mu DOUBLE

Median of beta distribution for methylation level of CpG loci. In range [0..1]. Default: 0.6.

--meth-cg-sigma DOUBLE

Standard deviation of beta distribution for methylation level of CpG loci. In range [0..1]. Default: 0.03.

--meth-chg-mu DOUBLE

Median of beta distribution for methylation level of CHG loci. In range [0..1]. Default: 0.08.

--meth-chg-sigma DOUBLE

Standard deviation of beta distribution for methylation level of CHG loci. In range [0..1]. Default: 0.008.

--meth-chh-mu DOUBLE

Median of beta distribution for methylation level of CHH loci. In range [0..1]. Default: 0.05.

--meth-chh-sigma DOUBLE

Standard deviation of beta distribution for methylation level of CHH loci. In range [0..1]. Default: 0.005.